1. Compound identification
2. Identification of spectra

Michał Burdukiewicz:

• bioinformatyk (UMB, IBB PAN, BTU Cottbus-Senftenberg),
• 12 lat doświadczenia z R,
• Stowarzyszenie Wrocławskich Użytkowników R (stwur.pl),
• Fundacja Why R? (whyr.pl).

Mail: michalburdukiewicz@gmail.com

Sindelar, M., and Patti, G.J. (2020). Chemical Discovery in the Era of Metabolomics. J. Am. Chem. Soc. 142, 9097–9105.

Sindelar, M., and Patti, G.J. (2020). Chemical Discovery in the Era of Metabolomics. J. Am. Chem. Soc. 142, 9097–9105.

Li, Y., Kuhn, M., Gavin, A.-C., and Bork, P. (2020). Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. Bioinformatics 36, 1213–1218.

Mass spectrum of L-Glutamic acid (3TMS) measured on a Bruker impact II.

• complex identification of structural isomers.

Mass spectrum of D-Glutamic acid (3TMS) measured on a Bruker impact II.

• hard to identify structural isomers,
• instrument-dependent fragmentation patterns.

Oberacher, H., Pitterl, F., Siapi, E., Steele, B.R., Letzel, T., Grosse, S., Poschner, B., Tagliaro, F., Gottardo, R., Chacko, S.A., et al. (2012). On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library. 3. Focus on ion trap and upfront CID. Journal of Mass Spectrometry 47, 263–270.

• hard to identify structural isomers,
• instrument-dependent fragmentation patterns,
• complex relationship between molecular structure and fragmentation spectra.

Databases: MassBank, MoNAi, METLIN and mzCloud.

Different search algorithms allow searching spectral databases with various levels of sensitivity and specificity.

Two compounds yielding the same set of ions at the same intensities due to similarity in structure and fragmentation pathways.

Stein, S. (2012). Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification. Anal. Chem. 84, 7274–7282.

Entirely different structures yielding ions of the same formulas,

Stein, S. (2012). Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification. Anal. Chem. 84, 7274–7282.

The same low mass ions from a substructure in common (benzoyl) for two very different precursor molecules.

Stein, S. (2012). Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification. Anal. Chem. 84, 7274–7282.

“Only 1.8% of spectra in an untargeted metabolomics experiment can be annotated.”

Silva, R.R. da, Dorrestein, P.C., and Quinn, R.A. (2015). Illuminating the dark matter in metabolomics. PNAS 112, 12549–12550.

QCEIMS: Born-Oppenheimer molecular dynamics.

Weakness: computational cost.

Ásgeirsson, V., Bauer, C.A., and Grimme, S. (2017). Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules. Chem. Sci. 8, 4879–4895.

Enumerate all possible fragments of candidate structures by systematic bond cleavage.

E.g., MIDAS-G, MetFrag, MAGMa+.

Use simulated fragmentation libraries to define rules of fragmentation for highly similar compounds.

E.g., Mass Frontier, LipidBlast, LipidMatch.

Fragmentation can be seen as a stochastic homogeneous Markov process (e.g., CFM-ID., NEIMS.